Not quite. The 1954 Johnson Amendment (legislated law) & the current IRS policy (crafted by bureaucrats) supposedly premised upon the 1954 Johnson Amendment are two different animals. As such the potential challenges are twofold (Constitutionality & Comportment with law it's supposedly premised upon) as evidenced when SCOTUS ruled 5-4 for Hobby Lobby in Burwell v. Hobby Lobby ruling that the mandated funding of contraception policy violated the Obamacare law it was supposedly premised upon
Regardless, I'm quite sure that the specific IRS policy has never been legally challenged and as such never made it to SCOTUS. In fact, the IRS has made a point of not enforcing or backing off each & every time a challenge seemed likely or possible & right now there are religious groups intentionally violating the policy & sending documentation of said violations to the IRS in hopes of being penalized & then having basis to mount a challenge. (see: Pulpit politics: Pastors endorse candidates, thumbing noses at the IRS
The IRS is all about intimidation with this policy and only those allowing themselves to be intimidated are being limited by the policy